The difference is that with the on the fly cert, you blindly trust one piece of code, at one point in time, and when it did not lie to you then you will be safe from it later. A conventional cert owner on the other hand could theoretically turn on you any time (e.g. when ownership multiplies into pwnership) once "automatic trust" for the next binary is established.
I'd still prefer the latter, given reasonable standards in terms of key handling, but the one-time trust is not completely without merit. It would certainly be more reasonable though to just allow one-time blind trust without forcing the installer to create a certificate that may or may not be as private as advertised.